The prognosis in patients with idiopathic membranous nephropathy (IMN) is diverse. However, the prognosis after relapse and factors affecting relapse remain unclear. A total of 146 Japanese patients with IMN who had been followed up for at least 3 years, or until end-stage renal failure or death were enrolled in this retrospective study. The initial clinicopathological factors were examined between the patients with and without relapse. The patients were assigned to two groups based on the electron microscopic findings: homogeneous type with synchronous electron-dense deposits and heterogeneous type with various phases of dense deposits. A total of 105 of the 146 patients (72 %) achieved complete remission (CR) or incomplete remission (ICR) I after initial treatment. Twenty-six of the 105 patients relapsed after CR or ICR I (25 %). There were no differences in initial clinical findings or data between the patients with and without relapse, except for the higher degree of proteinuria at onset in patients with relapse. The relapse rate of the heterogeneous group (43 %) was higher than that in the homogeneous group (20 %). There were no significant associations between relapse rate and immunosuppressive therapy at onset. Eleven of 26 patients showing relapse (42 %) achieved CR or ICR I, which was lower than the rate for patients with initial remission. Our results suggest that patients with relapse achieved CR or ICR I and that electron microscopic findings demonstrating heterogeneous type indicated susceptibility to relapse.